Humans have coevolved with microbial partners that constitutively inhabit all our barrier tissues including lung, skin and gut. To understand alterations leading to pathology and to provide targets for treatment and prevention, an integrated analysis of human physiology is needed to study humans as metaorganisms composed of a mixture of host and microbial cells with their own genes (metagenome) and shared metabolic processes and products (metabolome). The microbiota plays a central role in the maintenance and control of host homeostasis and can contribute to tissue inflammation. The NIAID Microbiome Program is supporting the work of NIAID intramural investigators focusing on microbiome research and is responsible for 3 main structures, the NIAID Gnotobiotic Animal Facility, the NIAID Microbiome Sequencing Platform, and a Microbiology Core. These structures were developed to support NIAID research associated with the exploration of the Microbiome in health and diseases.